Rauscher, Martina (2018). Topology of genealogical trees - theory and application. PhD thesis, Universität zu Köln.

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Abstract

Still today, identifying loci, which underwent recent selective sweeps is a difficult task, since traces are typically obscured by other evolutionary and demographic factors, such as genetic drift or population bottleneck events. To detect candidate loci of selective sweeps, we take here an approach which considers the genealogical relationships among individuals and the topological properties of the inferred coalescent tree. Selective sweeps can produce highly unbalanced coalescent tree topologies in region close to a selective sweep site. Building on a previously known test statistic called T3, which detects bias in the balance of binary genealogical trees, we derive a new test statistic based on a log likelihood approach and we call it the LR_T3-test. We present the results of genome wide screens of the LR_T3-test applied to the 26 populations of the phase 3 data set of the human 1,000 genomes project. Furthermore, we present a measure of topological linkage disequilibrium (tLD), which is based on clustering individuals with respect to their position in the genealogy rather than clustering alleles and haplotypes. We demonstrate its application to the beforehand processed human data.

Item Type: Thesis (PhD thesis)
Creators:
CreatorsEmailORCID
Rauscher, Martinamartina.rauscher@uni-koeln.deUNSPECIFIED
URN: urn:nbn:de:hbz:38-90303
Subjects: Data processing Computer science
Life sciences
Uncontrolled Keywords:
KeywordsLanguage
human population genetics; 1k genomes project; selective sweep; positive selection; coalescent tree topology; likelihood method; linkage disequilibrium; topological linkage disequilibrium;English
Faculty: Faculty of Mathematics and Natural Sciences
Divisions: Faculty of Mathematics and Natural Sciences > Institute for Genetics
Language: English
Date: 2018
Date of oral exam: 26 October 2018
Referee:
NameAcademic Title
Wiehe, ThomasProf. Dr.
Nothnagel, MichaelProf. Dr.
Refereed: Yes
URI: http://kups.ub.uni-koeln.de/id/eprint/9030

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